Australia and Indonesia were involved in a mid-ocean stand-off in the early hours of Friday morning as a customs vessel tried unsuccessfully to return a boatload of rescued asylum seekers to a reluctant Indonesia.

Australian authorities are liaising with their Indonesian counterparts in relation to a vessel that has requested assistance as the vessel is within Indonesia's Search and Rescue zone

Up to 56 asylum seekers were rescued from their wooden boat in Indonesia’s search and rescue zone by an Australian ship on Thursday and, rather than taking them to Christmas Island, the crew sought to return them to Indonesia.

A number of boatloads of asylum seekers have been returned in similar circumstances since the election of the Abbott government.

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But late on Thursday night a spokesman for Djoko Suyanto, the Indonesian co-ordinating minister for Legal, Political and Security Affairs, told Fairfax Media: “At least for the time being we will not accept them, since we consider them to be asylum seekers”.

The spokesman, Agus Barnas, said negotiations were continuing into the early hours of Friday morning and, meanwhile, the asylum seekers were still on their wooden boat with an Australian customs vessel standing by.

Immigration minister Scott Morrison’s office confirmed the stand-off, releasing a one-line statement saying: ''Australian authorities are liaising with their Indonesian counterparts in relation to a vessel that has requested assistance as the vessel is within Indonesia's search and rescue zone.''

The Australian Customs department and the Australian Maritime Safety Authority, which co-ordinated the rescue earlier on Thursday, refused to comment.

Labor's immigration spokesman, Richard Marles, said the government's response was not good enough.

''This just highlights how preposterous this information-management program that is being undertaken by Minister Morrison really is,'' Mr Marles told ABC radio on Friday.

He said that it was ''completely inappropriate'' that the Australian media first learned from Indonesian authorities about the participation of an Australian navy vessel in the rescue.

Mr Marles said the Australian public should be immediately informed of any involvement in the intervention of asylum-seeker vessels.

''We need to see a culture of transparency rather than a culture of secrecy,'' he said.

An Indonesian government source said the incident was now being supervised by Indonesia's high-powered Ministry for Politics, Security, Law and Human Rights and the Foreign Affairs Ministry, suggesting it has become an intensely political case.

On at least two occasions since the election of the Abbott government, asylum seekers rescued by Australian ships have been returned to Indonesian agencies in mid-ocean, ship-to-ship operations.

However, with tensions high over allegations of Australia spying on Indonesia, and no agreement reached yet on a co-operative way of dealing with asylum seekers, the Indonesians may have grown reluctant to accommodate Australian demands.

If the stand-off continues into Friday morning, it will represent a significant ramping up of tensions between the two governments, despite Tony Abbott’s election promise to make the relationship with Indonesia the warmest it had ever been.

Both foreign affairs minister Julie Bishop and defence minister David Johnston are due to meet their Indonesian counterparts on Indonesian soil on Friday morning.

Adi Fachroni Azis, the deputy officer in charge at Indonesian search and rescue agency Basarnas, confirmed that Australia had originally made the call to return the passengers to Indonesia.

Mr Adi said the Australian Rescue Coordination Centre had notified the Indonesians of a distress call from a wooden asylum seeker boat about 57 nautical miles south of Indonesia about 9.30am AEDT on Thursday morning.

The boat had reported engine trouble. But when HMAS Ballarat arrived about three hours later, the crew found the engine was in working order, so the Australian navy vessel sailed away.

It's understood an Australian ship then joined the vessel to ensure its safety.

It's unclear if the people aboard the boat sabotaged the engine after the Ballarat left them, but if they did, it would highlight the risk of any Australian policy of attempting to turn-back even seaworthy boats to Indonesia.

However, Mr Agus flagged the possibility to Fairfax Media of increased Indonesian navy patrols in the Timor Sea to intercept asylum boats.

That goodwill implicit in that offer seems to have dissipated since revelations emerged that Australia was involved in systematically spying on Indonesia's political elite.

345 comments

Indonesia stand your ground! I would do the same. I hope they join Europe with the new spy treaties that Europe are sketching together. I support Australias defense but that doesn't excuse asking a friend for help with "OUR" refugee problem and then spying on them as well. I hope Indonesia goes full throttle. Australia must be stopped before it thinks can get away with anything.

Commenter

The Other Guy1

Date and time

November 08, 2013, 6:37AM

Absolutely fantastic !

Better than any Labor add, this will really hit home to all those wanting to jump on boats. Indonesia will give in. All probably planned you leftie latte set.

Commenter

abc

Date and time

November 08, 2013, 6:55AM

Why is it"OUR" refugee problem?

Commenter

Parto

Date and time

November 08, 2013, 7:00AM

How is it our problem when they were in Indonesia's search and rescue zone?

Commenter

MJ

Location

Queensland

Date and time

November 08, 2013, 7:00AM

There is nothing for Indonesia to give in. Indonesia already said it doesn't have to give information to Australia. Indonesia is already in talks with Europe to join their countries against spying and create anti spy laws. Good for them I say. We like to ask people to remove covers off their faces when saying things and we call them cowards when doing so because they don't. Australia cannot have it both ways for once. Time for Australia to learn.

Commenter

The Other Guy1

Date and time

November 08, 2013, 7:02AM

Do you think Indonesia does not spy on us as well? Are you really that naive?

Commenter

adrian

Date and time

November 08, 2013, 7:04AM

The Indos have Abbott over a barrel. Not surprising - it's the same barrel that voters scraped the bottom of to give him the job. Unsophisticated, anti-intellectual, anti-science, tactless, gormless. He and his cronies might think he is a leader but unfortunately for Australia, the title is a very poor fit.

Commenter

errol

Date and time

November 08, 2013, 7:10AM

It's about time this was the news.. Not that another 800 illegals made it to Christmas Island!! The LNP are standing by their election promise and stopping the boats. Glad they got my vote :)

Commenter

Dave from Cairns

Date and time

November 08, 2013, 7:13AM

@abc. Play nice. Insulting others who disagree with your views on asylum seekers does not make for a rational debate. In fact, I see a lot of one-eyed supporters insulting another poster rather than addressing the issue. In this case, the issue is how well Australia is going with its new 'stop the boats' policy. Is it working?

Commenter

Ellie

Date and time

November 08, 2013, 7:14AM

So Australian navy vessels can operate freely in Indonesian sovereign waters - have they turned off their electronic surveillance equipment? No? The Indonesians are playing petty politics with their own wooden fishing boats. This is a disgrace. Bishop should summons the Indonesian Ambassador immediately and tell them that we won't patrol their sovereign waters.